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In silico characterization of Wall-Associated kinases (WAKs) in Populus trichocarpa

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HAL Id: hal-01268819

https://hal.archives-ouvertes.fr/hal-01268819

Submitted on 5 Jun 2020

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In silico characterization of Wall-Associated kinases (WAKs) in Populus trichocarpa

Kévin Tocquard

To cite this version:

Kévin Tocquard. In silico characterization of Wall-Associated kinases (WAKs) in Populus trichocarpa.

17th Docotral school for life sciences, Health, Agronomy and Environment Days, Ecole Doctorale des Sciences de la Vie et de la Santé. FRA., May 2014, Clermont-Fd, France. 1 p. �hal-01268819�

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Introduction

The wall-associated kinases (WAKs) are a set of receptor-like kinases (RLKs) involved in signaling pathways. WAKs have been described exhaustively in two herbaceous models, Arabidopsis thaliana and Oryza sativa (27 et 125 members, respectively). Various studies suggested that WAKs are able to bind pectins of the plant cell wall through a specific protein domain located in their extracellular region.

In woody species, WAKs, as receptors, may play a decisive part in development and in response to environmental constraints. The main characteristic of trees is wood production through secondary growth and perennialism, which implies short-term and long-lasting responses in continually changing environmental conditions. In addition, environmental stresses can induce specific modifications in secondary cell wall characteristics, notably G layer deposition in the tension wood, which requires cellular communications between the apoplasm and the cytoplasm. The involvement of WAKs as potential mediators of the reaction wood formation in response to gravitropic stimulus has been proposed.

In silico characterization of Wall-Associated Kinases (WAKs) in Populus trichocarpa

Tocquard Kévin Supervisors

Pr Roeckel-Drevet Patricia Dr Venisse Jean-Stéphane

He et al., 1999

cell wall cytoplasm signal peptide

EGF-like repeats

transmembrane domain kinase

Retrieval and sorting of PtWAK sequences

GubWAK WAK

EGFs T

M Kinase

WAKassoc

Protein domains

- GubWAK : adhesion site of WAKs to pectin - WAK : unknown function

- WAKassoc : unknown function

- EGFs : potentially involved in protein-protein interaction - TM : Transmembrane domain

- Kinase : phosphorylating domain

Extracellular

Intracellular

Group Specifications Gene number

PtWAK-RLK

(Receptor-like kinase) 119

PtWAK-RLCK

(Receptor-like cytoplasmic kinase) 32

PtWAK-RLP

(Receptor-like protein) 22

PtWAK short genes 2

Total number of WAKs 175

or or

0.1

Color ranges:

Poplar Rice

Arabidopsis

Potri.T112900.1

Potri.015G045100.1

Potri.015G044700.1 Potri.015G044800.1 Potri.T113200.1 Potri.T113100.1

Potri.012G054800.1 Potri.012G054700.1 Potri.010G120800.1

Potri.010G121100.1

Potri.017G118100.1 Potri.T064100.1

Potri.004G097100.1 Potri.004G096600.1

Potri.004G096900.1 Potri.017G118400.1

Potri.T064000.1 OsWAK1

OsW

AK10a

OsW

AK10b OsW

AK10c OsW

AK2 AtW

AKL21 AtW

AKL14

Potri.014G

038600.1

Potri.002G

130600.1

Potri.007G

034500.1

Potri.005G

130900.1 OsW

AK25

OsW AK

47 OsW

AK 59 OsW

AK 45 OsW

AK 49 OsW

AK 57

OsW

AK 42 OsW

AK 60 OsW

AK 46 OsW

AK 44

OsW

AK 43

OsW AK

51 OsW

AK 5 OsW

AK 8

OsW AK

64 OsW

AK 65

OsW AK

63 OsW

AK 12 OsW

AK 13

OsW AK

80

OsW

AK77 OsW

AK21 OsW

AK O 22

sWAK 24

OsWAK117 OsWAK116

OsWAK69

OsWAK123 OsWAK121

OsW

AK97 OsW

AK95 OsW

AK104

OsWAK 103 OsW

AK105 OsWAK

114

OsWAK99 OsWAK108 OsWAK

110

OsWAK126 OsWAK129a OsWAK26

OsWAK27

OsWAK61 OsWAK11

Potri.004G191500.1 Potri.004G191800.1

Potri.004G192400.1

Potri.004G192700.1 Potri.T167400.1

Potri.004G192900.1 Potri.004G191900.1 Potri.004G192100.1

Potri.004G193100.1 Potri.009G154100.1

Potri.009G154600.1

AtW AK L1 6

AtWAK3

AtW AK 1

AtW AK 5

AtW

AK

4

AtW AK

2

Po tri.002G

075900 .1 Po

tri.002G 076000

.1 AtWAKL22

AtWAKL2 AtWAKL4 AtWAKL5

AtWAKL1

AtWAKL3 AtWAKL10

AtWAKL9 AtWAKL13

AtWAKL17 AtWAKL18

AtWAKL11

AtWAKL8 Potri.009G154500.1 Potri.009G154300.1

Potri.009G157200.1

Potri.009G155000.1 Potri.003G186100.1 Potri.001G040800.1

Potri.T166600.1 Potri.001G040500.1

Potri.001G039200.1

Potri.001G038300.1 Potri.T132900.1

Potri.001G039900.1 Potri.T132800.1

Potri.T132700.1 Potri.001G041000.1 Potri.001G040900.1

Potri.001G040000.1 Potri.001G041100.1

Potri.T080500.1 Potri.00

3G185800.1

Potri.T080900.1 Potri.003G185700.1

Potri.004G192300.1 Potri.004G192500.1 Potri.T080700.1 Potri.T080600.1

Potri.003G186000.1

Potri.003G186200.1

Potri.T126500.1 Potri.018G148300.1

Potri.T126700.1

OsW AK29 OsW

AK28 OsW

AK6 OsW

AK9 OsW

AK56 OsW

AK14 OsW

AK15 OsW

AK16

OsW AK38 OsW

AK111 OsW

AK112b OsW

AK112d OsW

AK112a OsW

AK112c

OsW AK 75

OsW AK 87 OsW

AK73 OsW

AK76

OsW AK74 OsW

AK92 OsW

AK90 OsW

AK20 OsW

AK89a

OsW AK91 OsW

AK89b

OsW

AK55

OsWAK53a OsWAK53b Potri.006G118500.1

AtWAKL15

AtWAKL20

Potri.006G090200.1 Potri.008G059900.1

Potri.0

15G018

000.1 Potri.T

1364 00.1

Potri.0 12G

0034 00.1 Potri.0

12G 0035

00.1 Potri.012G

0028 00.1 Potri.012G

0030 00.1 Potri.T

1365 00.1 Potri.015G

0182 00.1 Potri.T

136600.1

Potri.017G

034700.1 Potri.017G

035500.1 Potri.007G

126200.1 Potri.007G

125100.1 Potri.007G

125600.1

Potri.0 12G

0546 00.1 Potri.T

1130 00.1 Potri.T

1128 00.1 Potri.0

15G 0452

00.1 Po

tri.017G 116900

.1 Po

tri.004G 097000

.1

Po tri.T

064900

.1 P otri.T

065000 .1

Po tri.017G

117500 .1

Po tri.T

064600 .1 Po

tri.017G 117300

.1 Po

tri.T 065200

.1 Po

tri.017G 117700

.1 Po

tri.T 064400

.1 Potri.0

10G 1209

00.1

Potri.0 10G

1210 00.1 Potri.0

04G 0764

00.1

Potri.0 04G

0765 00.1

Po tri.017G

034600

.1 P otri.017G

034500 .1

Po tri.017G

035400 .1

Po tri.0 07 G125500

.1 P otri. 00 7G 12 54 00 .1

Po tri.0 07 G125800

.1

Po tri.0 07 G1 25 20 0.1

Po tri.0 07 G1 25 00 0.1

Potri.015G018600.1 Potri.T136800.1

Potri.007G140900.1 Potri.007G140800.1

Potri.017G009600.1 Potri.017G009500.1

Potri.017G008000.1

Potri.017G009000.1

Potri.017G009200.1

Potri.017G008600.1 Potri.017G008200.1

Potri.017G007900.1

Potri.017G008400.1 Potri.017G008700.1

Potri.017G009400.1 Potri.017G009100.1

Po tri.0 07 G1 41 10 0.1 Po tri.0 07 G1 41 00 0.1

Potri.007G141500.1 Potri.007G141400.1 Po

tri.0 07 G1 17 00 0.1 Po tri.0 07 G1 17 10 0.1

Po tri.010G

118300 .1

Po tri.008G

125500 .1 Clade I

Clade II

Phylogenetic analyses

Phylogenetic tree of poplar WAKs

The protein domain architecture is indicated on the right of the phylogeny. Bar length and color shapes are proportional to the number of amino acids and the prediction of domain length, respectively. The tree obtained by the Bayesian inference method is represented.

Phylogenetic tree of poplar, rice and Arabidopsis WAKs

The tree obtained by the Bayesian inference method is represented.

Two monophyletic clades are markedly differentiated (i.e. WAK Clades I and II). A phylogenetic analysis of poplar, rice and Arabidopsis WAKs was also carried out.

WAK clade I contains members from the three species while WAK clade II contains only PtWAKs. This suggests that the evolution of sequences in the WAK clade I occurred in the monocot-dicot common ancestor, while the sequence in the WAK clade II evolved independently in poplar.

2.6 1.3 0.0

Potri.017G008700 Potri.015G045200 Potri.001G040500 Potri.T132900 Potri.017G034700 Potri.017G035500 Potri.009G154100 Potri.001G040000 Potri.017G118400

Potri.007G141100_Potri.007G141000 Potri.002G076000

Potri.017G035400 Potri.012G003000 Potri.017G117500

Potri.017G117200_Potri.017G117100 Potri.012G002800

Potri.012G003500 Potri.007G126200 Potri.004G191400 Potri.017G009200 Potri.014G038600 Potri.T064100 Potri.008G059900

Potri.007G140900_Potri.007G140800 Potri.004G191900

Potri.002G130600 Potri.004G191800 Potri.001G038300 Potri.005G130900 Potri.003G186100 Potri.005G203300 Potri.012G003700 Potri.004G192100 Potri.017G009400 Potri.T080500 Potri.015G018100 Potri.018G148300 Potri.007G125900 Potri.007G125100 Potri.007G125800 Potri.015G018600 Potri.017G009100

0.0 0.5 1.0

1.0 1.1 1.2

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Transcriptomics data analyses

WAK Clade I

WAK Clade II

 Although the phylogenetic analysis is calculated on the kinase domain, some monophyletic groups preferentially contained one type of extracellular domain combination, suggesting a parallel evolution between the intracellular kinase domain and extracellular domains of PtWAK-RLK.

Conclusion

WAKs features described above make WAKs appealing candidates to investigate new communication networks that may relay the cell wall status to the cytoplasm. The cell wall is an essential compartment affected by many biotic constrains such as pathogen attacks or developmental processes but also by abiotic stresses such as drought and various mechanical stimulations.

Our study provides new insights into the WAK gene family in Populus. Our findings may be a starting point for a study of the physiological roles of WAKs in cellular regulatory networks in woody species.

References

Tocquard K, Lafon-Placette C, Auguin D, Muries B, Bronner G, Lopez D, Fumanal B, Franchel J, Bourgerie S, Maury S, Label P, Julien JL, Roeckel-Drevet P, Venisse JS (2014) In silico study of wall-associated kinase family reveals large- scale genomic expansion potentially connected with functional diversification in Populus. Tree Genetics &

Genomes. DOI: 10.1007/s11295-014-0748-7.

Tocquard K, Lopez D, Decourteix M, Thibaut B, Julien JL, Label P, Leblanc-Fournier N, Roeckel-Drevet P (2014) The molecular mechanism of reaction wood induction. The biology of reaction wood. Springer Berlin Heidelberg, p 107- 138

Clustered heatmap showing expression patterns of significant tissue/condition/genotype specific expressed in poplar

Only PtWAKs showing differential expression in at least one tissue/environmental condition/genotype are displayed (42 PtWAKs). Scale from 0.0 to 1.0 corresponds to drought experiment in the apex; scale from 1.0 to 1.2 is for all the Affymetrix array experiments. An asterisk indicates significant tissue/environmental condition/genotype effect on PtWAK expression according to Welch’s t-test/one-way ANOVA for two or more samples followed by adjusted Bonferroni correction (* p < 0.05). Hierarchical clustering was performed for PtWAKs according to their expression patterns.

‘Carpaccio’, ‘DN34’ and ‘Soligo’ are Populus canadensis genotypes, ‘NM36’ is P. nigra × P. maximowiczii while ‘AP-947’, ‘AP-1005’, ‘AP-1006’, ‘AP-2278’,

‘AP-2298’ and ‘AP-2300’ are P. balsamifera genotypes. Blue- and red-shaded PtWAK names belong to PtWAK-RLK and PtWAK-RLCK gene groups, respectively.

Twenty-five PtWAKs showed a differential expression in at least on tissue, mainly an over-expression in mature leaves, roots and flowers, 16 PtWAKs were significantly affected by changing environmental conditions, and 24 were modulated differentially between poplar genotypes.

 Interestingly, PtWAK that showed a modulated expression after pathogen attack and PtWAK that are modulated during developmental/growth processes belong to WAK clade II (specific to poplar) and WAK clade I (shared with Arabidopsis and rice), respectively. This is in accordance with what have been shown for the global receptor-like kinase (RLK) family, suggesting that members of a gene family developed in a species-specific way correspond to species-specific needs.

Collaborations

Références

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